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A New Theory of Evolution

I invite you to consider…

What if evolution were true, but it wasn’t quite like Darwin said?charles_darwin_vegan_soldier_c

What if there were a new evolutionary model that could explain why fossils show almost no change for millions of years…. then suddenly the Cambrian Explosion: Thousands of new species emerge intact, virtually overnight.

What if this new theory pointed the way to new innovations in artificial intelligence and adaptive computer programs?

What if “Evolution vs. Design” wasn’t an either/or proposition – but both+and?

What if, instead of arguing endlessly about fossils, we could precisely track evolutionary history with the precision of 1’s and 0’s?

Read more »

Can Anybody Actually Win The Evolution 2.0 Prize?

evonne_crayonsCan Anybody Actually Win The Evolution 2.0 Prize?

Science, God, and

Happy Chemical Accidents

 

There’s a million codes out there. HTML, bar codes, zip codes, Java, English and Chinese.

Out of a million codes, 999,999 are designed by humans.

There’s one code we don’t know the origin of – and that’s DNA. We don’t know of any codes that are not designed. This implies design in DNA.

That’s an unsolved science mystery. So I and a group of Private Equity Investors have formed a company, Natural Code LLC, to offer a multi-million dollar technology prize for Origin Of Information.

Read more »

Evolution: The Untold Story, Part 1

There are two kinds of evolution:

1) There’s the version that you read about in the bookstore. It’s two-thirds science fiction.

2) Then there’s the version that PhD biologists, cancer researchers and genetic engineers use to do their jobs.

The two are entirely different.

Popular books tell you evolution works like this: Read more »

Do Epigenetic Changes Become Hard-Coded?

On April 22 2017, Jonathan McLatchie was kind enough to host me on his Apologetics Academy video livecast. We enjoyed a lively discussion about Evolution 2.0.

Generally, Jonathan and his audience were skeptical of macro-evolution and common descent. We discussed what Intelligent Design is, and what it is not; and how ID relates to evolution. I insisted that macro-evolution demands a higher view of God… a God that does not have to keep coming back and introducing new life forms on earth.

As I say in Evolution 2.0: “Darwinists underestimate nature. Creationists underestimate God.”

Midway through the show, a caller asked about epigenetics.

Layman’s explanation of epigenetics from Evolution 2.0:

In the Dutch famine of 1944 during World War II, thousands of unborn children experienced harsh deprivation, which resulted in unexpected changes. Not only were the children who were in utero during the famine smaller; when these children grew up and had children, their children were also smaller than average. Over their lifetime, the children of the famine experienced far-above-average rates of obesity, type 2 diabetes, cardiovascular problems, and other diseases related to an unhealthy body weight.

This data suggests that the famine experienced by the mothers triggered epigenetic changes that were inherited by the next generation.

Epigenetics doesn’t just alter the metabolism of children conceived in times of famine, though. It controls the expression of every cell in your body. The reason you have hair on the top of your head and not your forehead is because epigenetic factors control the expression of hair differently in different areas of your skin. It’s also the reason identical twins with identical DNA can still have different allergies, intelligence, aptitudes, and even different inherited diseases.

Epigenetics is blade #3 of the Evolution 2.0 Swiss Army Knife. It’s a switch that “grays out” genes, altering DNA’s function without changing the DNA sequence itself. It produces different cell types in fetal development; it alters tissues based on the external environment, and passes learned traits to offspring.

I suggested to her that it may be possible for epigenetic changes to become hard-coded into the genome over time, so that temporary adaptations become permanent. She challenged me on this. I promised to get back to her. Here’s what I found.

First, some further explanation of epigenetics, from Evolution 2.0:

I can take a sentence and make it say the opposite of what it said before, just by selectively “graying out” words and phrases:

Flight 6429 was delayed from Chicago to Winnipeg so it will not be departing before 6:45 P.M.

Flight 6429 was delayed from Chicago to Winnipeg so it will not be departing before 6:45 P.M.

(“Flight 6429 was from Winnipeg.”)
Flight 6429 was delayed from Chicago to Winnipeg so it will not be

departing before 6:45 P.M. 
(“Flight 29 to Winnipeg will depart before 6.”)

This illustrates how Epigenetics works—by “graying out” DNA sequences and making them silent. The mechanism that grays out the code is called methylation.

So… can this temporary graying-out of genes (which happens all the time, in response to external threats – things like callouses, temperature swings and a thousand other things) become hard-coded and permanent? Is epigenetics a powerful force for long-term evolution?

From correspondence with James Shapiro of the University of Chicago:

You are describing the fascinating but mysterious phenomenon discovered by Waddington known as “genetic assimilation.” Waddington treated Drosophila embryos to induce epigenetic changes producing flies with two pairs of wings (Bithorax).

After doing this for a few generations and mating the phenotypically altered flies, he discovered he no longer needed to treat the embryos. They had acquired Bithorax mutations in their genomes!

I’m not sure this has been replicated, and I’m not aware whether the mutations were ever subjected to detailed analysis. Nonetheless, Waddington’s observations have been widely cited and gained broad credibility from his status as the father of modern epigenetics.

Epigenetics is the interface between the organism and its environment.

See Shapiro’s 2011 book Evolution: A View from the 21st Century for a broader explanation of how cells rewrite their genomes in response to a dynamically changing environment.

From Epigenetic Inheritance: A Contributor to Species Differentiation?

…how extensive, and how stable, is the information carried in the germline by the epigenome? Several known examples of epigenetic inheritance demonstrate that it has the ability to create selectable traits, and thus to mediate Darwinian evolution. Here we discuss the possibility that epigenetic inheritance is responsible for some stable characteristics of species…

From Transgenerational Epigenetics by Trygve Tollefsbol:

Differentially expressed versions of a single allele have the potential to create an undetermined assortment of phenotypic novelties. Moreover, this increased phenotypic variation, observed within only a few generations, has the potential to play an important role in long-term evolutionary change, accelerating population divergence and driving speciation.

Methods for incorporating the parameterization of epiallelic instability in order to accurately reflect the variability of germline epigenetic modifications have no been established. These theoretical models have revealed how transgenerational epigenetic inheritance has the potential to profoundly affect usual evolutionary trajectories and result in elevated levels of phenotypic variation that would otherwise be unaccounted for under a standard population-genetic model. It has therefore been proposed that the Mendelian model requires amending in order to accommodate the transmission of “soft inheritance” alongside traditional genetic inheritance.

Although DNA methylation has been the focus of most of this research, many stably inherited epigenetic variants are believed to be caused by small RNAs, or perhaps a combination of different interacting epigenetic mechanisms. These data suggest that the composition or level of RNA in germ cells or associated cells could lead to a partial retention of epigenetic states down generations – through a combination of transmission stability and maternal effects…

From Epigenetics and Evolution by Mendizabal, Keller, Zeng and Soojin

The epigenome constitutes the interface between an organisms’ genome and its environment. Environmental factors such as chemicals, nutritional factors, or pathogens can alter the epigenetic landscape. A well-known example is how nutrition can determine the caste system in honey bees (Kucharski et al. 2008)

From: Friend or Foe: Epigenetic Regulation of Retrotransposons in Mammalian Oogenesis and Early Development by Alexei Evsikov, Caralina Marín de Evsikova

Bridging the realms of genetics and epigenetics, transposons are genetic elements regulated by epigenetic factors at biochemical and molecular levels.

TEs [Transposable Elements, discovered by Barbara McClintock] bridge genetic and epigenetic landscapes because TEs are genetic elements whose silencing and de-repression are regulated by epigenetic mechanisms that are sensitive to environmental factors. Ultimately, transposition events can change size, content, and function of mammalian genomes. Thus, TEs act beyond mutagenic agents reshuffling the genomes, and epigenetic regulation of TEs may act as a proximate mechanism by which evolutionary forces increase a species’ hidden reserve of epigenetic and phenotypic variability facilitating the adaptation of genomes to their environment.

…in mammalian genomes, experimental evidence supports epigenetic regulation of transposons as being critical to initiate synchronous, temporal expression of genes in germline, early embryos, and stem cells…

…living organisms developed and continue reinventing mechanisms for TE silencing, mostly via epigenetic mechanisms, which spares removal of TE loci from their genome…

TRANSLATION: Epigenetics gives an organism an ability to switch on a reserve of hidden programmed responses. Transposable Elements change the expression of genes and closely interact with epigenetic changes to coordinate adaptations to a constantly changing environment. Epigenetic switches can silence TEs and alter gene expression.

From Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives by Warren Burggren:

In a few more extreme, yet illustrative examples, epigenetically-inherited phenotypes caused by RNA interference persist across as many as 50 generations in Caenorhabditis elegans [34,58,110,111]. In the plant toadflax, epigenetically-inherited phenotypes are said to persist across possibly hundreds of generations [59]. Thus, the mere persistence of a modified phenotype across as many generations as most investigators have the patience to wait for is in and of itself insufficient evidence for the fixation of epigenetically-modified traits into the genome. Yet, there is evidence and theoretical arguments for both the direct and indirect involvement of epigenetics altering the genome, as will now be considered.

Confounding the determination of the role of epigenetics in evolution and speciation is the key question of whether epigenetically-acquired phenotypic traits themselves can actually become fixed intact, i.e. permanently added to the genome, as opposed to having the markers that generate them have indirect influence on the subsequent genome through genome destabilization, mutation, natural selection or other mechanisms. Mechanisms by which this might occur are emerging, but evidence remains somewhat circumstantial [4,19,27,119].

Importantly, it is not required for the epigenetically-inherited phenotype to become fixed into the genotype to affect the evolution of traits.

TRANSLATION: Epigenetic changes can extend 50-100+ generations without becoming hard-coded into the genome! This doesn’t mean the hard coding doesn’t ever happen, and there are both anecdotal indications and mathematical models to suggest it does. In any case, epigenetic factors undoubtedly affect long-term evolution.

I very commonly find that Intelligent Design advocates have a knee-jerk reaction against the power of epigenetics, transposition, symbiogenesis etc to produce large scale changes.

This opposition puzzles me. Why? Because the capabilities of such mechanisms do not, per se, undercut the general ID proposition that there is ultimate intelligence involved. But intelligence is found in the cells themselves and this makes the entire question vastly more interesting. It makes it possible for natural forms of id (lower case i, lower case d) to offer testable hypotheses that can be scientifically verified.

It seems ID people are looking for the hand of God in differences between species. But the ability for organisms to engineer new species in response to their environment is far more impressive than a God who has to repeatedly inject new forms of life into the earth.

So… given how limited our models of these systems presently are, we can only benefit by giving each adaptive process the benefit of the doubt and studying how it works – as evidenced by the fact that this very question stands at the bleeding edge of current scientific knowledge. Seeing how it took me many hours to compile just the information you see here, there is much productive work to be done.

Instead of opposing evolution scientists, why not join in and help?

ID advocates, I invite you to stop standing skeptically with your arms crossed. Instead, delve into these fascinating topics of research. In them you will find the mysteries of life.

Who is in control? YOU? Or your Genes?

A man is charged with first degree murder. His attorney agrees the man committed the crime… but argues that the killer is innocent because wasn’t in control of his own actions. That the killing was a result of him being, as Richard Dawkins argues in The Selfish Gene, a lumbering robot programmed by his genes.

Does this reasoning make sense?

Denis Noble of Oxford University, author of Dance to the Tune of Life: Biological Relativity and The Music of Life explores the consequences of reductionist philosophy at Oxford’s Rhodes House lecture.

What do YOU think? Post your comments below –

 

An Evolutionary Signpost is Needed – Guest Post by James MacAllister

The joint meeting of the Royal Society and the British Academy of Science, New trends in evolutionary biology: biological, philosophical and social science perspectives was a rematch of sorts. The two sides had already exchanged views in a 2014 Nature Comment, “Does evolutionary theory need a rethink? Researchers are divided over what processes should be considered fundamental.”

The Nature Comment had been set up as point and counterpoint. Kevin Laland and colleagues, Tobias Uller, Marc Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka argued the point, “Yes, urgently. Without an extended evolutionary framework, the theory neglects key processes.

Gregory A. Wray, Hopi E. Hoekstra, Douglas J. Futuyma, Richard E. Lenski, Trudy F. C. Mackay, Dolph Schluter, Joan E. Strassmann argued the counterpoint, “No, all is well. Theory [Modern Synthesis] accommodates evidence through relentless synthesis.

I had attended the joint meeting of the Royal Society and British Academy (RA-BA) before NASA researcher, Lynn Rothschild, brought the Nature Comment to my attention. What struck me about both the meeting and the Comment was the fact that the proponents of a “constantly synthesizing” version of the Modern Synthesis had failed to present a statement of their theory. This was not a minor detail, but such a glaring omission. I wondered how the editors of Nature had allowed what was going to be debated to remain completely undefined.

Similarly, the organizers Read more »

Jerry Coyne Evades Evolution 2.0

I got this question from an inquisitive reader:

I’m wrestling with some essential Jerry Coyne here. I figure this is pretty fundamental and therefore worth my taking the time to understand better.

Coyne says:

What we mean by “random” is that mutations occur regardless of whether they would be good for the organism. That is, the chances of an adaptive mutation occurring is not increased if the environment changes in a way that would favor that mutation.  The word “random” does not, to evolutionists, mean that every gene has the same chance of mutating, nor that mutation rates can’t be affected by other things. What it means is that mutation is not somehow adjusted so that good mutations crop up just when they would be advantageous. My friend Paul Sniegowski, a professor at Penn, uses the term “indifferent” instead of “random,” and I think that’s a better way to describe the neo-Darwinian view of mutations.

– What Coyne says is actually consistent with how you and Denis Noble and others define “random,” yes? no?

No.
 
Coyne is saying: ‘OK, mutation patterns are not Read more »

Francis Collins on Faith vs. Science

FRANCIS COLLINS, U.S. DIRECTOR OF THE HUMAN GENOME PROJECT: “Will we turn our backs on science because it is perceived as a threat to God, abandoning all the promise of advancing our understanding of nature and applying that to the alleviation of suffering and the betterment of humankind?

“Alternatively, will we turn our backs on faith, concluding that science has rendered the spiritual life no longer necessary, and that traditional religious symbols can now be replaced by engravings of the double helix on our altars?

“Both of these choices are profoundly dangerous. Both deny truth. Both will diminish the nobility of humankind. Both will be devastating to our future. And both are unnecessary. The God of the Bible is also the God of the genome. He can be worshipped in the cathedral or in the laboratory. His creation is majestic, awesome, intricate and beautiful—and it cannot be at war with itself. Only we imperfect humans can start such battles. And only we can end them.”

Photo by: National Center for Advancing Translational Sciences

Nassim Nicholas Taleb on Synthetic Life

“At the time of this writing, the biologist Craig Venter is engaging in the creation of artificial life. He conducted experiments and stated them in a famous paper titled “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.”

“I have an immense respect for Craig Venter, whom I consider one of the smartest men who ever breathed, and a “doer” in the full sense of the word, but giving fallible humans such powers is similar to giving a small child a bunch of explosives.

“If I understand this well, to the creationists, this should be an insult to God; but further, to the evolutionist, this is certainly an insult to evolution. And to the probabilist, like myself and my peers, this is an insult to human prudence, the beginning of the mother of all exposures to Black Swans.”
-Nassim Nicholas Taleb, from his book “Antifragile.”

 

How Trees Talk To Each Other – Suzanne Simard

“A forest is much more than what you see,” says ecologist Suzanne Simard. Her 30 years of research in Canadian forests have led to an astounding discovery — trees talk, often and over vast distances. Learn more about the harmonious yet complicated social lives of trees and prepare to see the natural world with new eyes.

Is Intelligent Design really just Old Earth Creationism?

I got this astute blog comment from Frank Morris:

“I was so impressed by your debate with Stephen Meyer that I finally bought your Evolution 2.0 book. I can’t wait to read it to see how it compares with my own journey getting kicked around by hostile Darwinians on blogs as I continued to question their seemingly crazy theory.

“Stephen Meyer, on the other hand, was profoundly disappointing. I rejected ID over 10 years ago, but I always thought that, in principle, the concept of ID accepted any form of intelligent cause, not just the God answer. The reality of cellular intelligence has forced the Discovery Institute to expose their bluff. Dr. Meyer seems to be trying to change it from ID to OD, a step up to Omniscient Design.

“He’s wrong. Omniscient means all-knowing. Cells, who are clearly rearranging their own genomes, are very intelligent, but not omniscient.

“Cells are not gods, as another responder suggested. They are intelligent little critters trying their best to survive, but they don’t simply know all things by omniscience. They use internal homeostatic systems, environmental monitoring systems and intercellular communication to establish their needs and responses to need. So they need to SEEK information about their external and internal status, which means they don’t just magically know all things. On top of that is the lack of the perfection one would expect of omniscience. Thanks for the article.”

I replied back to Frank:

Read more »

Richard Rohr on Evolution

“The universe really is “inspirational matter,” we now know, and is not merely inert. Now we might call it instinct, evolution, nuclear fusion, DNA, hardwiring, the motherboard, healing, growth, or just springtime, but nature clearly continues to renew itself from within.

“God seems to have created things that continue to create and recreate themselves from the inside out. It is no longer God’s one-time creation or evolution; rather, God’s form of creation precisely is evolution.”

-Fr.Richard Rohr, from his book Falling Upward

Are Cells Intelligent?

I had a great exchange with a gentleman, Matthew Taylor, on the Unbelievable discussion board, following my debate with Stephen Meyer.

Matthew said:

I was intrigued by the suggestion by one of the guests that cells might have some form of intelligence.

I’d like to know what experiments and tests have been proposed so that evidence of this intelligence can be shown and measured. It’s all well and good coming up with far out ideas like that, but if they can’t be demonstrated there is little point is trying to build an idea based on the hypothesis. It would be far more honest to prove the claim before trying to build an idea on it.

I replied:
Read more »

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Discover the 70-Year-Old Nobel Prize-winning discovery that rendered old-school Darwinism obsolete.

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Discover the 70-Year-Old Nobel Prize-winning discovery that rendered old-school Darwinism obsolete.

Get 3 Free Chapters of "Evolution 2.0 via Email".
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Darwin Bad
Evolution Good 
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Rub 2 rocks together and create a cell with DNA... that's evolution, right?
Learn the truth.
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Lava. Gas. Water.
Life?
Discover the truth.


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Discover the 70-Year-Old Nobel Prize-winning discovery that rendered old-school Darwinism obsolete.

Get 3 Free Chapters of "Evolution 2.0 via Email".

Click anywhere outside the form to close.